PD-1 Expression during Acute Infection Is Repressed through an LSD1-Blimp-1 Axis

During prolonged exposure to Ags, such as chronic viral infections, sustained TCR signaling can result in T cell exhaustion mediated in part by expression of programmed cell death-1 (PD-1) encoded by the Pdcd1 gene. In this study, dynamic changes in histone H3K4 modifications at the Pdcd1 locus during ex vivo and in vivo activation of CD8 T cells suggested a potential role for the histone H3 lysine 4 demethylase LSD1 in regulating PD-1 expression. CD8 T cells lacking LSD1 expressed higher levels of Pdcd1 mRNA following ex vivo stimulation as well as increased surface levels of PD-1 during acute, but not chronic, infection with lymphocytic choriomeningitis virus (LCMV). Blimp-1, a known repressor of PD-1, recruited LSD1 to the Pdcd1 gene during acute, but not chronic, LCMV infection. Loss of DNA methylation at Pdcd1's promoter-proximal regulatory regions is highly correlated with its expression. However, following acute LCMV infection, in which PD-1 expression levels return to near baseline, LSD1-deficient CD8 T cells failed to remethylate the Pdcd1 locus to the levels of wild-type cells. Finally, in a murine melanoma model, the frequency of PD-1-expressing tumor-infiltrating LSD1-deficient CD8 T cells was greater than in wild type. Thus, LSD1 is recruited to the Pdcd1 locus by Blimp-1, downregulates PD-1 expression by facilitating the removal of activating histone marks, and is important for remethylation of the locus. Together, these data provide insight into the complex regulatory mechanisms governing T cell immunity and regulation of a critical T cell checkpoint gene.

Progressive Upregulation of Oxidative Metabolism Facilitates Plasmablast Differentiation to a T-Independent Antigen

Transitioning from a metabolically quiescent naive B cell to an antibody-secreting plasmablast requires division-dependent cellular differentiation. Though cell division demands significant ATP and metabolites, the metabolic processes used for ATP synthesis during plasmablast formation are not well described. Here, the metabolic requirements for plasmablast formation were determined. Following T-independent stimulation with lipopolysaccharide, B cells increased expression of the oxidative phosphorylation machinery in a stepwise manner. Such activated B cells have increased capacity to perform oxidative phosphorylation but showed dependency on glycolysis. Plasmablasts displayed higher oxidative metabolism to support antibody secretion, as inhibiting oxidative ATP production resulted in decreased antibody titers. Differentiation by Blimp1 was required for this increase in oxidative metabolism, as Blimp1-deficient cells proliferate but do not upregulate oxidative phosphorylation. Together, these findings identify a shift in metabolic pathways as B cells differentiate, as well as the requirement for increased metabolic potential to support antibody production.

Understanding and measuring human B-cell tolerance and its breakdown in autoimmune disease

The maintenance of immunological tolerance of B lymphocytes is a complex and critical process that must be implemented as to avoid the detrimental development of autoreactivity and possible autoimmunity. Murine models have been invaluable to elucidate many of the key components in B-cell tolerance; however, translation to human homeostatic and pathogenic immune states can be difficult to assess. Functional autoreactive, flow cytometric, and single-cell cloning assays have proven to be critical in deciphering breaks in B-cell tolerance within autoimmunity; however, newer approaches to assess human B-cell tolerance may prove to be vital in the further exploration of underlying tolerance defects. In this review, we supply a comprehensive overview of human immune tolerance checkpoints with associated mechanisms of enforcement, and highlight current and future methodologies which are likely to benefit future studies into the mechanisms that become defective in human autoimmune conditions.

IgM, IgG, and IgA Influenza-Specific Plasma Cells Express Divergent Transcriptomes

Ab-secreting cells (ASC) or plasma cells are essential components of the humoral immune system. Although Abs of different isotypes have distinct functions, it is not known if the ASC that secrete each isotype are also distinct. ASC downregulate their surface BCR upon differentiation, hindering analyses that couple BCR information to other molecular characteristics. In this study, we developed a methodology using fixation, permeabilization, and intracellular staining coupled with cell sorting and reversal of the cross-links to allow RNA sequencing of isolated cell subsets. Using hemagglutinin and nucleoprotein Ag-specific B cell tetramers and intracellular staining for IgM, IgG, and IgA isotypes, we were able to derive and compare the gene expression programs of ASC subsets that were responding to the same Ags following influenza infection in mice. Intriguingly, whereas a shared ASC signature was identified, each ASC isotype-specific population expressed distinct transcriptional programs controlling cellular homing, metabolism, and potential effector functions. Additionally, we extracted and compared BCR clonotypes and found that each ASC isotype contained a unique, clonally related CDR3 repertoire. In summary, these data reveal specific complexities in the transcriptional programming of Ag-specific ASC populations.

Phosphoinositide 3-Kinase Signaling Can Modulate MHC Class I and II Expression

Molecular events activating the PI3K pathway are frequently detected in human tumors and the activation of PI3K signaling alters numerous cellular processes including tumor cell proliferation, survival, and motility. More recent studies have highlighted the impact of PI3K signaling on the cellular response to interferons and other immunologic processes relevant to antitumor immunity. Given the ability of IFNγ to regulate antigen processing and presentation and the pivotal role of MHC class I (MHCI) and II (MHCII) expression in T-cell-mediated antitumor immunity, we sought to determine the impact of PI3K signaling on MHCI and MHCII induction by IFNγ. We found that the induction of cell surface MHCI and MHCII molecules by IFNγ is enhanced by the clinical grade PI3K inhibitors dactolisib and pictilisib. We also found that PI3K inhibition increases STAT1 protein levels following IFNγ treatment and increases accessibility at genomic STAT1-binding motifs. Conversely, we found that pharmacologic activation of PI3K signaling can repress the induction of MHCI and MHCII molecules by IFNγ, and likewise, the loss of PTEN attenuates the induction of MHCI, MHCII, and STAT1 by IFNγ. Consistent with these in vitro studies, we found that within human head and neck squamous cell carcinomas, intratumoral regions with high phospho-AKT IHC staining had reduced MHCI IHC staining. IMPLICATIONS: Collectively, these findings demonstrate that MHC expression can be modulated by PI3K signaling and suggest that activation of PI3K signaling may promote immune escape via effects on antigen presentation.

LSD1 Cooperates with Noncanonical NF-κB Signaling to Regulate Marginal Zone B Cell Development

Marginal zone B cells (MZB) are a mature B cell subset that rapidly respond to blood-borne pathogens. Although the transcriptional changes that occur throughout MZB development are known, the corresponding epigenetic changes and epigenetic modifying proteins that facilitate these changes are poorly understood. The histone demethylase LSD1 is an epigenetic modifier that promotes plasmablast formation, but its role in B cell development has not been explored. In this study, a role for LSD1 in the development of B cell subsets was examined. B cell-conditional deletion of LSD1 in mice resulted in a decrease in MZB whereas follicular B cells and bone marrow B cell populations were minimally affected. LSD1 repressed genes in MZB that were normally upregulated in the myeloid and follicular B cell lineages. Correspondingly, LSD1 regulated chromatin accessibility at the motifs of transcription factors known to regulate splenic B cell development, including NF-κB motifs. The importance of NF-κB signaling was examined through an ex vivo MZB development assay, which showed that both LSD1-deficient and NF-κB-inhibited transitional B cells failed to undergo full MZB development. Gene expression and chromatin accessibility analyses of in vivo- and ex vivo-generated LSD1-deficient MZB indicated that LSD1 regulated the downstream target genes of noncanonical NF-κB signaling. Additionally LSD1 was found to interact with the noncanonical NF-κB transcription factor p52. Together, these data reveal that the epigenetic modulation of the noncanonical NF-κB signaling pathway by LSD1 is an essential process during the development of MZB.

T-bet Transcription Factor Promotes Antibody-Secreting Cell Differentiation by Limiting the Inflammatory Effects of IFN-γ on B Cells

Although viral infections elicit robust interferon-γ (IFN-γ) and long-lived antibody-secreting cell (ASC) responses, the roles for IFN-γ and IFN-γ-induced transcription factors (TFs) in ASC development are unclear. We showed that B cell intrinsic expression of IFN-γR and the IFN-γ-induced TF T-bet were required for T-helper 1 cell-induced differentiation of B cells into ASCs. IFN-γR signaling induced Blimp1 expression in B cells but also initiated an inflammatory gene program that, if not restrained, prevented ASC formation. T-bet did not affect Blimp1 upregulation in IFN-γ-activated B cells but instead regulated chromatin accessibility within the Ifng and Ifngr2 loci and repressed the IFN-γ-induced inflammatory gene program. Consistent with this, B cell intrinsic T-bet was required for formation of long-lived ASCs and secondary ASCs following viral, but not nematode, infection. Therefore, T-bet facilitates differentiation of IFN-γ-activated inflammatory effector B cells into ASCs in the setting of IFN-γ-, but not IL-4-, induced inflammatory responses.

IFNγ induces epigenetic programming of human T-bethi B cells and promotes TLR7/8 and IL-21 induced differentiation

Although B cells expressing the IFNγR or the IFNγ-inducible transcription factor T-bet promote autoimmunity in Systemic Lupus Erythematosus (SLE)-prone mouse models, the role for IFNγ signaling in human antibody responses is unknown. We show that elevated levels of IFNγ in SLE patients correlate with expansion of the T-bet expressing IgDnegCD27negCD11c+CXCR5neg (DN2) pre-antibody secreting cell (pre-ASC) subset. We demonstrate that naïve B cells form T-bethi pre-ASCs following stimulation with either Th1 cells or with IFNγ, IL-2, anti-Ig and TLR7/8 ligand and that IL-21 dependent ASC formation is significantly enhanced by IFNγ or IFNγ-producing T cells. IFNγ promotes ASC development by synergizing with IL-2 and TLR7/8 ligands to induce genome-wide epigenetic reprogramming of B cells, which results in increased chromatin accessibility surrounding IRF4 and BLIMP1 binding motifs and epigenetic remodeling of IL21R and PRDM1 loci. Finally, we show that IFNγ signals poise B cells to differentiate by increasing their responsiveness to IL-21.

IRF4 regulates the proliferative response during B cell differentiation in vivo

Cell division is an essential component of B cell differentiation to a plasma cell (PC). Division coupled changes in the expression of transcription factors that coordinate the PC program are known; however, little is known regarding the timing/extent of reprogramming by these factors as the cells are dividing in vivo. Furthermore, how/when these factors coordinate cell division during differentiation has remained unexplored. To address this, we assessed the cell division kinetics of wild-type (WT) B cells responding to LPS in vivo. Interestingly, we found that WT B cells must undergo 8 divisions before differentiating into PCs. Computational modeling of division rates defined a proliferative burst between 48 and 60 hours after LPS injection that is characterized by a rapid increase in the rate of cell division. In contrast, Interferon Regulatory Factor 4-deficient (IRF4−/−) B cells divided but stalled at divisions 2–6, failing to undergo the proliferative burst. To assess the timing/scope of IRF4-dependent reprogramming, WT and IRF4−/− responding B cells at divisions 0, 1, and 3–6 were sorted for ATAC- and RNA-seq. RNA-seq data revealed hundreds of differentially expressed genes (DEGs) when IRF4 was deleted, a subset of which included Myc target genes. ATAC-seq data also exposed hundreds of differentially accessible regions (DARs), the majority of which contained a known IRF4 binding motif and mapped to a corresponding DEG. Interestingly, IRF4−/− B cells progressively became more divergent as they divided when compared to WT B cells in the same division. Together, these data create a road map defining the role of IRF4 throughout B cell differentiation and reveal a critical role for IRF4 in maintaining the proliferative response.

Epigenetic programming underpins B cell dysfunction in human SLE

Systemic lupus erythematosus (SLE) is characterized by the expansion of extrafollicular pathogenic B cells derived from newly activated naïve cells. Although these cells have distinct markers and phenotypes, their epigenetic architecture and how it contributes to SLE remains poorly understood. To establish if epigenetic mechanisms contributed to pathogenic B cell programming in SLE, we systematically determined the DNA methylation, chromatin accessibility and transcriptome landscape of human B cell subsets from SLE and healthy subjects. To comprehensively cover the B cell lineage, we isolated resting naïve, activated subsets, class-switched memory, plasmabasts, and a newly defined effector B cell subset. These data define a differentiation hierarchy between the subsets and elucidate the epigenetic and transcriptional differences between effector and memory B cells. Intriguingly, an SLE epigenetic signature was already established in resting naïve cells and persisted in more differentiated subsets. DNA methylation profiling revealed a set of CpG surrounding IFN response genes whose methylation status were highly predictive of disease activity. The AP-1 and EGR transcription factor networks were highly enriched in the SLE accessible chromatin and dysregulated genes. Together, these transcription factors acted in synergy with TBET to shape the epigenome of expanded SLE effector B cell subsets. These results provide insights into the epigenetic programming of human B cell subsets, identify loci that correlate with the expansion of distinct pathogenic B cell subsets, and suggest that early alterations in the epigenome may predispose B cells towards a disease fate.

PD-1 is negatively regulated by LSD1 through interactions with Blimp-1 during acute viral infection

Prolonged exposure to antigen, such as during chronic viral infections and cancer, leads to sustained TCR signaling and ultimately T cell exhaustion, which is in part mediated by up regulation of Programmed cell death 1 (PD-1). Antibody blockade of PD-1 does not work in all instances and can lead to autoimmunity, thus identifying novel tools to manipulate PD-1 are needed. Therefore, we sought to understand the genetic and epigenetic mechanisms that regulate PD-1 during acute and chronic antigen conditions in order to identify additional therapeutic targets to modulate PD-1. We determined the chromatin status at the PD-1 locus and found that activating H3K4me1 and H3K4me2 epigenetic modifications were still present at day 8 during a chronic but not acute LCMV infection. This suggested a failure to remove the active histone marks in chronic infections. Indeed, CD8 T cells lacking lysine-specific histone demethylase 1A (LSD1), a H3K4 demethylase, display significantly higher levels of PD-1 mRNA and protein during acute but not chronic infection. Molecular analysis revealed that Blimp-1 recruits LSD1 to the PD-1 locus to induce silencing during acute infection. Despite Blimp-1 binding to the PD-1 locus during both acute and chronic LCMV infection, it fails to recruit LSD1 during the chronic setting. Additionally, failure to remove H3K4 methylation resulted in less DNA methylation at known PD-1 control regions compared to wild-type cells, consistent with the differential expression of PD-1. Taken together, these results demonstrate that LSD1 downregulates PD-1 by interacting with Blimp-1 during acute, but not chronic LCMV infection, facilitating full epigenetic repression of the locus.

Three-dimensional localization spectroscopy of individual nuclear spins with sub-Angstrom resolution

Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for analyzing the chemical composition and molecular structure of materials. At the nanometer scale, NMR has the prospect of mapping the atomic-scale structure of individual molecules, provided a method that can sensitively detect single nuclei and measure inter-atomic distances. Here, we report on precise localization spectroscopy experiments of individual 13C nuclear spins near the central electronic sensor spin of a nitrogen-vacancy (NV) center in a diamond chip. By detecting the nuclear free precession signals in rapidly switchable external magnetic fields, we retrieve the three-dimensional spatial coordinates of the nuclear spins with sub-Angstrom resolution and for distances beyond 10 Å. We further show that the Fermi contact contribution can be constrained by measuring the nuclear g-factor enhancement. The presented method will be useful for mapping atomic positions in single molecules, an ambitious yet important goal of nanoscale nuclear magnetic resonance spectroscopy.

Distinct Effector B Cells Induced by Unregulated Toll-like Receptor 7 Contribute to Pathogenic Responses in Systemic Lupus Erythematosus

Systemic Lupus Erythematosus (SLE) is characterized by B cells lacking IgD and CD27 (double negative; DN). We show that DN cell expansions reflected a subset of CXCR5^- CD11c⁺ cells (DN2) representing pre-plasma cells (PC). DN2 cells predominated in African-American patients with active disease and nephritis, anti-Smith and anti-RNA autoantibodies. They expressed a T-bet transcriptional network; increased Toll-like receptor-7 (TLR7); lacked the negative TLR regulator TRAF5; and were hyper-responsive to TLR7. DN2 cells shared with activated naive cells (aNAV), phenotypic and functional features, and similar transcriptomes. Their PC differentiation and autoantibody production was driven by TLR7 in an interleukin-21 (IL-21)-mediated fashion. An in vivo developmental link between aNAV, DN2 cells, and PC was demonstrated by clonal sharing. This study defines a distinct differentiation fate of autoreactive naive B cells into PC precursors with hyper-responsiveness to innate stimuli, as well as establishes prominence of extra-follicular B cell activation in SLE, and identifies therapeutic targets.

The Histone Demethylase LSD1 Regulates B Cell Proliferation and Plasmablast Differentiation

B cells undergo epigenetic remodeling as they differentiate into Ab-secreting cells (ASC). LSD1 is a histone demethylase known to decommission active enhancers and cooperate with the ASC master regulatory transcription factor Blimp-1. The contribution of LSD1 to ASC formation is poorly understood. In this study, we show that LSD1 is necessary for proliferation and differentiation of mouse naive B cells (nB) into plasmablasts (PB). Following LPS inoculation, LSD1-deficient hosts exhibited a 2-fold reduction of splenic PB and serum IgM. LSD1-deficient PB exhibited derepression and superinduction of genes involved in immune system processes; a subset of these being direct Blimp-1 target-repressed genes. Cell cycle genes were globally downregulated without LSD1, which corresponded to a decrease in the proliferative capacity of LSD1-deficient activated B cells. PB lacking LSD1 displayed increased histone H3 lysine 4 monomethylation and chromatin accessibility at nB active enhancers and the binding sites of transcription factors Blimp-1, PU.1, and IRF4 that mapped to LSD1-repressed genes. Together, these data show that LSD1 is required for normal in vivo PB formation, distinguish LSD1 as a transcriptional rheostat and epigenetic modifier of B cell differentiation, and identify LSD1 as a factor responsible for decommissioning nB active enhancers.

B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation

B cells provide humoral immunity by differentiating into antibody-secreting plasma cells, a process that requires cellular division and is linked to DNA hypomethylation. Conversely, little is known about how de novo deposition of DNA methylation affects B cell fate and function. Here we show that genetic deletion of the de novo DNA methyltransferases Dnmt3a and Dnmt3b (Dnmt3-deficient) in mouse B cells results in normal B cell development and maturation, but increased cell activation and expansion of the germinal center B cell and plasma cell populations upon immunization. Gene expression is mostly unaltered in naive and germinal center B cells, but dysregulated in Dnmt3-deficient plasma cells. Differences in gene expression are proximal to Dnmt3-dependent DNA methylation and chromatin changes, both of which coincide with E2A and PU.1-IRF composite-binding motifs. Thus, de novo DNA methylation limits B cell activation, represses the plasma cell chromatin state, and regulates plasma cell differentiation.

IRF4 regulates the rate of cell cycle during B cell differentiation

Cell division is required for the initiation of B cell differentiation, the regulation of isotype class switching, and ultimately entry of cells into the plasma cell (PC) lineage. Division coupled changes in the expression of transcription factors, such as interferon regulatory factor-4 (IRF4), that coordinate the PC transcriptional program also occur; however, little is known regarding how these factors coordinate cell division and exit from the cell cycle after differentiation. To begin to address this gap in knowledge, we assessed the cell division kinetics of wildtype (WT) B cells responding to the T cell independent antigen lipopolysaccharide (LPS). Interestingly, we found that WT B cells undergo at least 8 divisions before differentiating into PCs. Computational modeling of division rates over time defined a proliferative burst between 48 and 60 hours after LPS injection that is characterized by a rapid increase in the rate of cell division. IRF4-deficient B cells divided but failed to undergo the proliferative burst resulting in fewer activated B cells. Indeed, IRF4 is expressed at low levels during these divisions before being upregulated in post-mitotic CD138+ PCs after 8 divisions. Notably, while more than 40% of WT B cells reached division 8+ by 72 hours, IRF4-null B cells appeared to be stalled at divisions 2–5. Taken together, these data suggest that IRF4 regulates the rate of cellular proliferation during B cell differentiation that occurs around divisions 2–5 and that this role may be concentration-dependent.

The histone demethylase LSD1 regulates B cell proliferation and plasmablast differentiation

In order to generate humoral immunity, B cells must differentiate into antibody-secreting cells in response to antigen. LSD1 is a histone demethylase that regulates multiple cellular differentiation pathways and has been implicated to function during B cell differentiation through interaction with Blimp-1. Here we show that LSD1 is necessary for maximal proliferation and differentiation of naïve B cells into LPS-induced plasmablasts. LSD1-deficient B cell differentiation results in the targeted upregulation of hundreds of genes, a subset being Blimp-1 repressed genes, as well as the targeted downregulation of cell cycle genes. Plasmablasts lacking LSD1 fail to close chromatin at naïve B cell active enhancers in addition to PU.1 and IRF4 binding sites. LSD1 directly regulates the Blimp-1 target gene Sell through H3K4me1 demethylation at its Blimp-1 target binding sites. Our data defines LSD1 as a critical transcriptional and epigenetic repressor in plasmablasts.

Cellular stress mediated by the local microenvironment regulates the homeostatic loss of tissue-resident memory CD8 T cells in different compartments of the lung

Lung-resident memory T cells (lung TRM) are important for protective heterosubtypic immunity against influenza viruses; however, the efficacy of this cellular immunity wanes over time. To better understand the mechanisms leading to the decline of protective cellular immunity, we investigated the long-term maintenance of airway and parenchyma lung TRM. In contrast to circulating flu-specific memory T cells and TRM in other tissues, lung TRM numbers in the airways and parenchyma steadily decline for several months following influenza infection. All flu-specific lung TRM decline at similar rates regardless of expression of the tissue residency markers CD69 and CD103. Parabiosis experiments demonstrate that established lung TRM in the airways or parenchyma do not freely interchange with circulating memory T cells. Thus the gradual loss of these cells is likely due to increased cell death in the tissue. In support of this, airway and parenchyma lung TRM show increased apoptosis compared to systemic flu-specific memory T cells during homeostasis. To identify epigenetic and transcriptional programs specific to lung TRM, we performed parallel RNA-seq and ATAC-seq on flu-specific memory CD8 T cells from the airways, lung parenchyma, and spleen. We found that lung TRM populations have increased expression of genes associated with cellular stress, and airway TRM in particular have a signature associated with amino acid starvation and ER stress. Finally, intratracheal transfer experiments determined that the airway environment was sufficient to program the lung TRM transcriptional signature. Together, these data show that the decline of lung TRM is a direct result of cellular stresses driven by the lung microenvironment.

LSD1 regulates PD-1 expression through interactions with Blimp-1 during acute viral infection

During prolonged exposure to antigens, such as during chronic viral infections, sustained T cell receptor (TCR) signaling via cognate peptide: MHC interactions results in T cell exhaustion mediated in part by the expression of Programmed cell death protein 1 (PD-1). PD-1 blockade has been implemented in the clinical setting as a promising treatment for several different forms of cancer and therefore obtaining a complete understanding of the epigenetic mechanisms that regulate PD-1 is of great value to improving existing therapies. Here, we demonstrate that CD8 positive T cells lacking lysine-specific histone demethylase 1A (LSD1) expressed approximately 2-fold higher levels of PD-1 mRNA following TCR stimulation. Antigen specific CD8 T cells lacking LSD1 also showed increased surface levels of PD-1 during acute infection with LCMV but not during chronic infection. Molecular analysis revealed that Blimp-1, a known repressor of PD-1, recruits LSD1 for silencing. Although Blimp-1 is able to bind the PD-1 locus during both acute and chronic LCMV infection, it fails to recruit LSD1 in the chronic setting. LSD1 is responsible for removing activating histone modifications H3K4me1 and H3K4me2 and our results show that these marks are removed from the PD-1 locus only during acute infection. During viral infection, loss of DNA methylation is associated with with PD-1 expression. Examination of the PD-1 locus during acute infection revealed that LSD1 null CD8 T cells had less methylation compared to cells expressing LSD1 further demonstrating the role of LSD1 in regulating PD-1 expression. Taken together, these results demonstrate LSD1 downregulates PD-1 by interactions with Blimp-1.

Progressive upregulation of oxidative metabolism facilitates plasmablast differentiation to a T-independent antigen

Transitioning from a metabolically quiescent naïve B cell to an antibody-secreting plasmablast requires division-dependent cellular differentiation. Though cellular processes such as cell division and antibody secretion demand significant ATP and metabolites, the metabolic processes used to generate ATP during plasmablast formation are not well described. Here, the metabolic machinery requirements for plasmablast formation were determined. Following T-independent stimulation with lipopolysaccharide, B cells increased expression of the oxidative phosphorylation machinery in a step-wise manner. Such activated B cells have increased capacity to perform oxidative phosphorylation, but showed additional dependency on glycolytic metabolism. Plasmablasts displayed higher oxidative metabolism to support antibody secretion, as inhibiting oxidative ATP production with oligomycin resulted in decreased antibody titres. Differentiation orchestrated by Blimp1 was required for this increase in oxidative metabolism as Blimp1-deficient cells proliferate normally, but neither differentiate to plasmablasts nor upregulate oxidative phosphorylation. Therefore, Blimp1 expression is required for full metabolic activity, and proliferation alone is insufficient to induce full oxidative phosphorylation. Together, these findings identify a shift in metabolic pathways as B cells differentiate, as well as the requirement for increased metabolic potential to support antibody production.

EZH2 Represses the B Cell Transcriptional Program and Regulates Antibody-Secreting Cell Metabolism and Antibody Production

Epigenetic remodeling is required during B cell differentiation. However, little is known about the direct functions of epigenetic enzymes in Ab-secreting cells (ASC) in vivo. In this study, we examined ASC differentiation independent of T cell help and germinal center reactions using mice with inducible or B cell-specific deletions of Ezh2 Following stimulation with influenza virus or LPS, Ezh2-deficient ASC poorly proliferated and inappropriately maintained expression of inflammatory pathways, B cell-lineage transcription factors, and Blimp-1-repressed genes, leading to fewer and less functional ASC. In the absence of EZH2, genes that normally gained histone H3 lysine 27 trimethylation were dysregulated and exhibited increased chromatin accessibility. Furthermore, EZH2 was also required for maximal Ab secretion by ASC, in part due to reduced mitochondrial respiration, impaired glucose metabolism, and poor expression of the unfolded-protein response pathway. Together, these data demonstrate that EZH2 is essential in facilitating epigenetic changes that regulate ASC fate, function, and metabolism.

High-Resolution Quantum Sensing with Shaped Control Pulses

We investigate the application of amplitude-shaped control pulses for enhancing the time and frequency resolution of multipulse quantum sensing sequences. Using the electronic spin of a single nitrogen-vacancy center in diamond and up to 10 000 coherent microwave pulses with a cosine square envelope, we demonstrate 0.6-ps timing resolution for the interpulse delay. This represents a refinement by over 3 orders of magnitude compared to the 2-ns hardware sampling. We apply the method for the detection of external ac magnetic fields and nuclear magnetic resonance signals of ^{13}C spins with high spectral resolution. Our method is simple to implement and especially useful for quantum applications that require fast phase gates, many control pulses, and high fidelity.

Ezh2 is required for the division-specific epigenetic programming of plasma cell differentiation

Following activation of naïve B cells, epigenetic remodeling is required to facilitate the induction of the plasma cell gene expression program. Ezh2 is an epigenetic repressor, catalyzing the trimetylated state of histone H3 lysine 27 (H3K27me3), and is essential for B cell development and the maintenance of a germinal center reaction. Recently, Ezh2 has been shown to directly interact with the master transcriptional regulator of plasma cell fate Blimp1. To investigate a wider role in regulating other aspects of B cell fate, a tamoxifen-inducible deletion of Ezh2 was developed, allowing deletion during distinct phases of B cell differentiation. Ezh2 was not required for mature B cell homeostasis, however; in response to differentiation signals, a cell-intrinsic reduction in antibody secreting plasma cells was observed. Additionally, Ezh2 deficient plasma cells secreted fewer antibodies, indicating a failure to fully induce the plasma cell fate. To determine the molecular processes regulated by Ezh2, chromatin accessibility and the transcriptome were profiled by ATAC-seq and RNA-seq, respectively. Ezh2 deficient plasma cells demonstrated an up regulation of inflammatory related genes and B cell lineage transcription factors. Chromatin accessibility data indicated a failure to repress B cell enhancers and promoters. Additionally, Blimp1 target genes displayed increased expression in Ezh2 deficient plasma cells providing a genetic link to the interaction of these two repressors. Together, these data indicate that Ezh2 facilitates the epigenetic repression of the B cell program and is required for full induction of plasma cell fate and function.

Pathogenic epigenetic programming of expanded B cell subsets in systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is characterized by multiple B cell abnormalities that contribute to disease pathogenesis through the production of autoantibodies. The recent characterizations of immune cells from SLE patients suggest that distinct B cell subsets are expanded and that defects in epigenetic programming may be a contributing factor to disease etiology. Using high-dimensional flow cytometry, five B cell subsets were isolated from cohorts of SLE and HC subjects. To create a molecular map of each cell type, the transcriptome was defined by RNA-seq and the epigenome by dual DNA methylation (RRBS) and chromatin accessibility (ATAC-seq) profiling. These data reveal cell-type relationships that suggest pathogenic B cell subsets are programmed to differentiate down a different trajectory than normal B cells. Across all SLE B cell subsets a distinct disease signature was observed in each of the three data sets. Resting naïve B cells displayed a similar SLE signature to expanded B cell subsets indicating that a disease programming exists early in the differentiation pathway. Distinct epigenetic footprints were identified for transcriptional networks active in SLE B cells, revealing the unique environmental signals these cells receive. These results provide insights into the molecular programming of human B cell subsets, identify loci that may contribute to the expansion of distinct pathogenic B cell subsets, and suggest that early alterations in programming predispose B cells towards a disease fate.

Oxidative phosphorylation is progressively programmed during plasma cell differentiation

The differentiation of immune cells requires a transition in metabolic programming to achieve effector function. Unlike T cells, the metabolic changes and epigenetic regulation of this process during the differentiation of antibody secreting plasma cells is not well characterized. Using in vivo and ex vivo LPS driven models of B cell differentiation, the metabolic changes and epigenetic regulation of metabolism was investigated. Naïve B cells (B220+GL7−CD138−) are metabolically quiescent, and upon activation through TLR4, B cells rapidly shift their metabolic program to use oxidative phosphorylation for their energetic demands. Activated B cells (B220+GL7+CD138−) use oxidative phosphorylation, but maintain a large spare respiratory capacity. In contrast, terminally differentiated, post-mitotic plasma cells (B220−GL7−CD138+) use oxidative phosphorylation at their maximal ability, with no spare respiratory capacity, suggesting unique metabolic changes are programmed upon differentiation. Next, an adoptive transfer model system that utilizes CFSE labeled B cells was used to distinguish molecular events during the proliferative/activation versus the differentiation phase. Analysis of epigenetic and transcriptome data in the two phases identified a subset of metabolic genes that underwent differentiation specific programming. Additionally, the role of key transcription factors was examined in terms of their control of the metabolic reprogramming steps. These results provide novel insights into how the step-wise changes in metabolism are programmed as quiescent B cells differentiate into antibody-secreting plasma cells.

TULIPES: Tn5-mediated ultra low input parallel epigenetic sequencing

Accumulating evidence reveals that changes in the epigenome regulate gene expression profiles of developing, differentiating, and effector immune cells. Importantly, disturbances in this developmental road map may contribute to aberrant immune responses. The recent development of the Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) allows for the epigenetic programming of rare immune cells to be determined. This method utilizes the Tn5 transposase to simultaneously fragment and tag genomic DNA by inserting Illumina sequencing adapters. Unique sequencing indexes are then added to the adapter-modified genomic fragments during the PCR enrichment step of sample preparation. This tagmentation-based approach has emerged as a popular approach to generating sequence-ready libraries. Here, we describe a novel strategy in which we have customized the tagmentation process by using in-house purified Tn5 transposase pre-loaded with indexed adapters. This method allows for a more efficient analysis of samples which increases experimental throughput while significantly reducing sequencing cost.

Inhibition of H3K27me3-specific demethylases promotes plasma cell formation

B cell terminal differentiation must be properly regulated to ensure robust humoral immune responses. In additional to the well-established role of key transcription factors, there is a growing interest in the epigenetic regulation of B cell differentiation. However, the epigenetic remodeling that occurs to suppress the B cell and promote the plasma cell fate is still poorly understood. Histone H3 lysine 27 trimethylation (H3K27me3) is a modification associated with a repressive chromatin state and gene silencing. H3K27me3 is established by EZH2 (component of PRC2) and was shown to be essential in the formation and maintenance of germinal centers. In addition, other studies have shown that active removal of silencing marks by H3K27me3-specific demethylases is necessary for T-cell differentiation. To further evaluate the role of H3K27me3 in plasma cell differentiation, we evaluated the effects of pharmacological inhibition of UTX and JMJD3 (H3K27me3-specific demethylases) in B cells stimulated ex vivo with LPS, IL2, and IL5 in the presence of the inhibitor or vehicle control. Our preliminary data suggest that retention of those silencing histone modifications nearly doubles the number of B220+ CD138+ plasma cells after 3-day ex vivo culture as assayed by flow cytometry. We also evaluated viability, gene expression profile, and functionality of the plasma cells treated with or without the inhibitor. Taken together, the collected data provide us with more insight into the role of H3K27me3 dynamics in B cell terminal differentiation.

ChIP-seq analysis of genomic binding regions of five major transcription factors highlights a central role for ZIC2 in the mouse epiblast stem cell gene regulatory network

To obtain insight into the transcription factor (TF)-dependent regulation of epiblast stem cells (EpiSCs), we performed ChIP-seq analysis of the genomic binding regions of five major TFs. Analysis of in vivo biotinylated ZIC2, OTX2, SOX2, POU5F1 and POU3F1 binding in EpiSCs identified several new features. (1) Megabase-scale genomic domains rich in ZIC2 peaks and genes alternate with those rich in POU3F1 but sparse in genes, reflecting the clustering of regulatory regions that act at short and long-range, which involve binding of ZIC2 and POU3F1, respectively. (2) The enhancers bound by ZIC2 and OTX2 prominently regulate TF genes in EpiSCs. (3) The binding sites for SOX2 and POU5F1 in mouse embryonic stem cells (ESCs) and EpiSCs are divergent, reflecting the shift in the major acting TFs from SOX2/POU5F1 in ESCs to OTX2/ZIC2 in EpiSCs. (4) This shift in the major acting TFs appears to be primed by binding of ZIC2 in ESCs at relevant genomic positions that later function as enhancers following the disengagement of SOX2/POU5F1 from major regulatory functions and subsequent binding by OTX2. These new insights into EpiSC gene regulatory networks gained from this study are highly relevant to early stage embryogenesis.

LRRK2 levels in immune cells are increased in Parkinson's disease

Mutations associated with leucine-rich repeat kinase 2 are the most common known cause of Parkinson’s disease. The known expression of leucine-rich repeat kinase 2 in immune cells and its negative regulatory function of nuclear factor of activated T cells implicates leucine-rich repeat kinase 2 in the development of the inflammatory environment characteristic of Parkinson’s disease. The aim of this study was to determine the expression pattern of leucine-rich repeat kinase 2 in immune cell subsets and correlate it with the immunophenotype of cells from Parkinson’s disease and healthy subjects. For immunophenotyping, blood cells from 40 Parkinson’s disease patients and 32 age and environment matched-healthy control subjects were analyzed by flow cytometry. Multiplexed immunoassays were used to measure cytokine output of stimulated cells. Leucine-rich repeat kinase 2 expression was increased in B cells (p = 0.0095), T cells (p = 0.029), and CD16⁺ monocytes (p = 0.01) of Parkinson’s disease patients compared to healthy controls. Leucine-rich repeat kinase 2 induction was also increased in monocytes and dividing T cells in Parkinson’s disease patients compared to healthy controls. In addition, Parkinson’s disease patient monocytes secreted more inflammatory cytokines compared to healthy control, and cytokine expression positively correlated with leucine-rich repeat kinase 2 expression in T cells from Parkinson’s disease but not healthy controls. Finally, the regulatory surface protein that limits T-cell activation signals, CTLA-4 (cytotoxic T-lymphocyte-associated protein 4), was decreased in Parkinson’s disease compared to HC in T cells (p = 0.029). In sum, these findings suggest that leucine-rich repeat kinase 2 has a regulatory role in immune cells and Parkinson’s disease. Functionally, the positive correlations between leucine-rich repeat kinase 2 expression levels in T-cell subsets, cytokine expression and secretion, and T-cell activation states suggest that targeting leucine-rich repeat kinase 2 with therapeutic interventions could have direct effects on immune cell function.

High levels of leucine-rich repeat kinase 2 (LRRK2) in immune cells disrupt immune system function in patients with Parkinson’s disease (PD). Mutations in LRRK2 are the most common genetic cause of PD. Although LRRK2 is found in many immune cells, research efforts have focussed on determining its effects on neuronal function. Malu G. Tansey at Emory University, USA, and colleagues compared the levels and function of LRKK2 in immune cells from 40 late-onset PD patients and 32 age- and environment-matched healthy controls. The cells from PD patients had higher levels of LRKK2 protein and produced more pro-inflammatory molecules in response to stimulation than the control cells. As exacerbated inflammatory responses are known to aggravate neurodegeneration, monitoring LRKK2 levels may aid the assessment of disease progression in both inherited and sporadic cases of PD.

Cutting Edge: Chromatin Accessibility Programs CD8 T Cell Memory

CD8 T cell memory is characterized by rapid recall of effector function, increased proliferation, and reduced activation requirements. Despite the extensive functional characterization, the molecular mechanisms that facilitate these enhanced properties are not well characterized. In this study, the assay for transposase-accessible chromatin sequencing was employed to map the cis-regulatory elements in CD8 T cells responding to acute and chronic lymphocytic choriomeningitis virus infections. Integration of chromatin accessibility profiles with gene expression data identified unique regulatory modules that were enriched for distinct combinations of transcription factor-binding motifs. Memory CD8 T cells displayed a chromatin accessibility structure that was absent from other acute and exhausted cells types and included key effector and proliferative genes. Stimulation of memory cells revealed enhanced transcription of "memory-primed" genes compared with naive cells. Thus, memory CD8 T cells display a preprogrammed chromatin accessibility profile and maintain a molecular history of cis-element usage, thereby reducing the steps necessary to revive effector functions.

Conserved Region C Functions To Regulate PD-1 Expression and Subsequent CD8 T Cell Memory

Expression of programmed death 1 (PD-1) on CD8 T cells promotes T cell exhaustion during chronic Ag exposure. During acute infections, PD-1 is transiently expressed and has the potential to modulate CD8 T cell memory formation. Conserved region C (CR-C), a promoter proximal cis-regulatory element that is critical to PD-1 expression in vitro, responds to NFATc1, FoxO1, and/or NF-κB signaling pathways. Here, a CR-C knockout mouse was established to determine its role on PD-1 expression and the corresponding effects on T cell function in vivo. Deletion of CR-C decreased PD-1 expression on CD4 T cells and Ag-specific CD8 T cells during acute and chronic lymphocytic choriomeningitis virus challenges, but did not affect the ability to clear an infection. Following acute lymphocytic choriomeningitis virus infection, memory CD8 T cells in the CR-C knockout mouse were formed in greater numbers, were more functional, and were more effective at responding to a melanoma tumor than wild-type memory cells. These data implicate a critical role for CR-C in governing PD-1 expression, and a subsequent role in guiding CD8 T cell differentiation. The data suggest the possibility that titrating PD-1 expression during CD8 T cell activation could have important ramifications in vaccine development and clinical care.

ZBTB32 Restricts the Duration of Memory B Cell Recall Responses

Memory B cell responses are more rapid and of greater magnitude than are primary Ab responses. The mechanisms by which these secondary responses are eventually attenuated remain unknown. We demonstrate that the transcription factor ZBTB32 limits the rapidity and duration of Ab recall responses. ZBTB32 is highly expressed by mouse and human memory B cells but not by their naive counterparts. Zbtb32(-/-) mice mount normal primary Ab responses to T-dependent Ags. However, Zbtb32(-/-) memory B cell-mediated recall responses occur more rapidly and persist longer than do control responses. Microarray analyses demonstrate that Zbtb32(-/-) secondary bone marrow plasma cells display elevated expression of genes that promote cell cycle progression and mitochondrial function relative to wild-type controls. BrdU labeling and adoptive transfer experiments confirm more rapid production and a cell-intrinsic survival advantage of Zbtb32(-/-) secondary plasma cells relative to wild-type counterparts. ZBTB32 is therefore a novel negative regulator of Ab recall responses.

Genetic and Epigenetic Regulation of PD-1 Expression

The inhibitory immune receptor programmed cell death-1 (PD-1) is intricately regulated. In T cells, PD-1 is expressed in response to most immune challenges, but it is rapidly downregulated in acute settings, allowing for normal immune responses. On chronically stimulated Ag-specific T cells, PD-1 expression remains high, leading to an impaired response to stimuli. Ab blockade of PD-1 interactions during chronic Ag settings partially restores immune function and is now used clinically to treat a variety of devastating cancers. Understanding the regulation of PD-1 expression may be useful for developing novel immune-based therapies. In this review, the molecular mechanisms that drive dynamic PD-1 expression during acute and chronic antigenic stimuli are discussed. An array of cis-DNA elements, transcription factors, and epigenetic components, including DNA methylation and histone modifications, control PD-1 expression. The interplay between these regulators fine-tunes PD-1 expression in different inflammatory environments and across numerous cell types to modulate immune responses.

One- and Two-Dimensional Nuclear Magnetic Resonance Spectroscopy with a Diamond Quantum Sensor

We report on Fourier spectroscopy experiments performed with near-surface nitrogen-vacancy centers in a diamond chip. By detecting the free precession of nuclear spins rather than applying a multipulse quantum sensing protocol, we are able to unambiguously identify the NMR species devoid of harmonics. We further show that, by engineering different Hamiltonians during free precession, the hyperfine coupling parameters as well as the nuclear Larmor frequency can be selectively measured with up to five digits of precision. The protocols can be combined to demonstrate two-dimensional Fourier spectroscopy. Presented techniques will be useful for mapping nuclear coordinates in molecules deposited on diamond sensor chips, en route to imaging their atomic structure.

Epigenetic regulation of histone H3 lysine 27 (H3K27) controls the division-specific timing of gene expression during B cell differentiation

The differentiation of B cells to plasma cells is required for the generation of a protective antibody response. Following activation, B cells undergo multiple rounds of cell division that result in progressive differentiation and the acquisition of plasma cell phenotypic traits. However, how the epigenetic program is remodeled to facilitate differentiation, what the cis-regulatory elements that participate in this process are, and the molecular timing of these events during cellular division are poorly understood. To dissect B cell differentiation in vivo, five distinct divisions, representing unique stages of B cell differentiation were isolated by FACS. The changes in chromatin landscape were identified by the Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) and the effects on gene expression measured by RNA-seq. In parallel, histone modification profiles in naïve B cells and plasmablasts were defined. Interestingly, the loci with losses and gains in the histone modifications H3K27ac and H3K27me3 were highly correlated with enhancer activity and gene expression changes. To investigate the role of H3K27me3, B cells were differentiated in the presence of GSK343, a small molecule inhibitor of H3K27me3. Plasma cells differentiated at earlier divisions in the absence of H3K27me3 and a three-fold increase total plasma cells was observed. Together these data define the division coupled epigenetic events that regulate B cell differentiation, provide the first map of plasma cell cis-regulatory elements, and identify epigenetic processes that regulate the timing of differentiation during division.

Common Genetic Variant Association with Altered HLA Expression, Synergy with Pyrethroid Exposure, and Risk for Parkinson's Disease: An Observational and Case-Control Study

Background:

The common noncoding single-nucleotide polymorphism (SNP) rs3129882 in HLA-DRA is associated with risk for idiopathic Parkinson’s disease (PD). The location of the SNP in the major histocompatibility complex class II (MHC-II) locus implicates regulation of antigen presentation as a potential mechanism by which immune responses link genetic susceptibility to environmental factors in conferring lifetime risk for PD.

Aims:

The aim of this study was to determine the effect of this SNP on the MHC-II locus and its synergy with pesticide exposure.

Methods:

For immunophenotyping, blood cells from 81 subjects were analyzed by quantitative reverse transcription-PCR and flow cytometry. A case–control study was performed on a separate cohort of 962 subjects to determine association of pesticide exposure and the SNP with risk of PD.

Results:

Homozygosity for G at this SNP was associated with heightened baseline expression and inducibility of MHC class II molecules in B cells and monocytes from peripheral blood of healthy controls and PD patients. In addition, exposure to a commonly used class of insecticide, pyrethroids, synergized with the risk conferred by this SNP (odds ratio=2.48, P=0.007), thereby identifying a novel gene–environment interaction that promotes risk for PD via alterations in immune responses.

Conclusions:

In sum, these novel findings suggest that the MHC-II locus may increase susceptibility to PD through presentation of pathogenic, immunodominant antigens and/or a shift toward a more pro-inflammatory CD4+ T-cell response in response to specific environmental exposures, such as pyrethroid exposure through genetic or epigenetic mechanisms that modulate MHC-II gene expression.

Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment

The class II transactivator (CIITA) is essential for the expression of major histocompatibility complex class II (MHC-II) genes; however, the role of CIITA in gene regulation outside of MHC-II biology is not fully understood. To comprehensively map CIITA-bound loci, ChIP-seq was performed in the human B lymphoblastoma cell line Raji. CIITA bound 480 sites, and was significantly enriched at active promoters and enhancers. The complexity of CIITA transcriptional regulation of target genes was analyzed using a combination of CIITA-null cells, including a novel cell line created using CRISPR/Cas9 tools. MHC-II genes and a few novel genes were regulated by CIITA; however, most other genes demonstrated either diminished or no changes in the absence of CIITA. Nearly all CIITA-bound sites were within regions containing accessible chromatin, and CIITA's presence at these sites was associated with increased histone H3K27 acetylation, suggesting that CIITA's role at these non-regulated loci may be to poise the region for subsequent regulation. Computational genome-wide modeling of the CIITA bound XY box motifs provided constraints for sequences associated with CIITA-mediated gene regulation versus binding. These data therefore define the CIITA regulome in B cells and establish sequence specificities that predict activity for an essential regulator of the adaptive immune response.

NF-κB regulates PD-1 expression in macrophages

Programmed cell death-1 (PD-1) is responsible for T cell exhaustion during chronic viral infections and is expressed on a variety of immune cells following activation. Despite its importance, the mechanisms that regulate PD-1 in cell types other than CD8 T cells are poorly defined. In this study, the molecular mechanisms for inducing PD-1 expression in CD4 T cells, macrophages, and B cells were explored. In CD4 T cells, PD-1 induction following TCR stimulation required NFAT, as the calcineurin/NFAT pathway inhibitor cyclosporin A was able to block PD-1 induction in a manner similar to that seen in CD8 T cells. In contrast, LPS but not PMA and ionomycin stimulation was able to induce PD-1 expression in macrophages in a manner insensitive to cyclosporin A-mediated inhibition. B cells could use both pathways, although the levels of PD-1 expression were highest with PMA and ionomycin. An NF-κB binding site located upstream of the gene in conserved region C was required for NF-κB-dependent PD-1 gene activation in macrophages. Chromatin immunoprecipitation showed NF-κB p65 binding to this region following stimulation of macrophages with LPS. PD-1 induction was associated with histone modifications characteristic of accessible chromatin; however, in contrast to CD8 T cells, conserved region B in macrophages did not lose CpG methylation upon stimulation and PD-1 expression. The linkage of TLR/NF-κB signaling to the induction of PD-1 suggests the possibility of an opportunistic advantage to microbial infections in manipulating immune inhibitory responses.

RETRACTED: Single-proton spin detection by diamond magnetometry

Extending magnetic resonance imaging to the atomic scale has been a long-standing aspiration, driven by the prospect of directly mapping atomic positions in molecules with three-dimensional spatial resolution. We report detection of individual, isolated proton spins by a nitrogen-vacancy (NV) center in a diamond chip covered by an inorganic salt. The single-proton identity was confirmed by the Zeeman effect and by a quantum coherent rotation of the weakly coupled nuclear spin. Using the hyperfine field of the NV center as an imaging gradient, we determined proton-NV distances of less than 1 nm.

Common distal elements orchestrate CIITA isoform-specific expression in multiple cell types

Major histocompatibility class II (MHC-II) expression is critical for immune responses and is controlled by the MHC-II transactivator CIITA. CIITA is primarily regulated at the transcriptional level and is expressed from three main promoters with myeloid, lymphoid, and IFN-γ treated non-hematopoietic cells using promoters pI, pIII, and pIV, respectively. Recent studies in non-hematopoietic cells suggest a series of distal regulatory elements may be involved in regulating CIITA transcription. To identify distal elements in B cells, a DNase I-hypersensitivity screen was performed, revealing a series of potential novel regulatory elements. These elements were analyzed computationally and biochemically. Several regions displayed active histone modifications and/or enhanced expression of a reporter gene. Four of the elements interacted with pIII in B cells. These same four regions were also found to interact with pI in splenic dendritic cells (spDC). Intriguingly, examination of the above interactions in pI-knockout-derived spDC showed a switch to the next available promoter, pIII. Extensive DNA methylation was found at the pI region in B cells, suggesting that this promoter is not accessible in B cells. Thus, CIITA expression is likely mediated in hematopoietic cells by common elements with promoter accessibility playing a part in promoter choice.

STAT3, STAT4, NFATc1, and CTCF regulate PD-1 through multiple novel regulatory regions in murine T cells

Programmed death-1 (PD-1) is a crucial negative regulator of CD8 T cell development and function, yet the mechanisms that control its expression are not fully understood. Through a nonbiased DNase I hypersensitivity assay, four novel regulatory regions within the Pdcd1 locus were identified. Two of these elements flanked the locus, bound the transcriptional insulator protein CCCTC-binding factor, and interacted with each other, creating a potential regulatory compartmentalization of the locus. In response to T cell activation signaling, NFATc1 bound to two of the novel regions that function as independent regulatory elements. STAT binding sites were identified in these elements as well. In splenic CD8 T cells, TCR-induced PD-1 expression was augmented by IL-6 and IL-12, inducers of STAT3 and STAT4 activity, respectively. IL-6 or IL-12 on its own did not induce PD-1. Importantly, STAT3/4 and distinct chromatin modifications were associated with the novel regulatory regions following cytokine stimulation. The NFATc1/STAT regulatory regions were found to interact with the promoter region of the Pdcd1 gene, providing a mechanism for their action. Together these data add multiple novel distal regulatory regions and pathways to the control of PD-1 expression and provide a molecular mechanism by which proinflammatory cytokines, such as IL-6 or IL-12, can augment PD-1 expression.

B cell differentiation is associated with reprogramming the CCCTC binding factor-dependent chromatin architecture of the murine MHC class II locus

The transcriptional insulator CCCTC binding factor (CTCF) was shown previously to be critical for human MHC class II (MHC-II) gene expression. Whether the mechanisms used by CTCF in humans were similar to that of the mouse and whether the three-dimensional chromatin architecture created was specific to B cells were not defined. Genome-wide CTCF occupancy was defined for murine B cells and LPS-derived plasmablasts by chromatin immunoprecipitation sequencing. Fifteen CTCF sites within the murine MHC-II locus were associated with high CTCF binding in B cells. Only one-third of these sites displayed significant CTCF occupancy in plasmablasts. CTCF was required for maximal MHC-II gene expression in mouse B cells. In B cells, a subset of the CTCF regions interacted with each other, creating a three-dimensional architecture for the locus. Additional interactions occurred between MHC-II promoters and the CTCF sites. In contrast, a novel configuration occurred in plasma cells, which do not express MHC-II genes. Ectopic CIITA expression in plasma cells to induce MHC-II expression resulted in high levels of MHC-II proteins, but did not alter the plasma cell architecture completely. These data suggest that reorganizing the three-dimensional chromatin architecture is an epigenetic mechanism that accompanies the silencing of MHC-II genes as part of the cell fate commitment of plasma cells.

Blimp-1 represses CD8 T cell expression of PD-1 using a feed-forward transcriptional circuit during acute viral infection

The transcription factor Blimp-1 represses PD-1 expression in effector CD8⁺ T cells during acute LCMV infection.

Programmed cell death 1 (PD-1) is an inhibitory immune receptor that regulates T cell function, yet the molecular events that control its expression are largely unknown. We show here that B lymphocyte–induced maturation protein 1 (Blimp-1)–deficient CD8 T cells fail to repress PD-1 during the early stages of CD8 T cell differentiation after acute infection with lymphocytic choriomeningitis virus (LCMV) strain Armstrong. Blimp-1 represses PD-1 through a feed-forward repressive circuit by regulating PD-1 directly and by repressing NFATc1 expression, an activator of PD-1 expression. Blimp-1 binding induces a repressive chromatin structure at the PD-1 locus, leading to the eviction of NFATc1 from its site. These data place Blimp-1 at an important phase of the CD8 T cell effector response and provide a molecular mechanism for its repression of PD-1.

DNA insertions which affect the expression of the yeast iso-2-cytochrome c gene

The plasmid YCpCYC7(2) was constructed containing the Saccharomyces cerevisiae CYC7 gene, encoding the iso-2-cytochrome c protein, replicative sequences and selective markers from both E. coli and yeast, and the centromere of yeast chromosome III. The expression of the plasmid-CYC7 gene in yeast was similar to the low level expression characteristic of the chromosomal CYC7 gene. A number of insertions into the sequences 5' to the gene were constructed in vitro. The insertion at 142 by 5' to the coding sequence of a 400 by fragment which lies 5' to the CYC1 gene and is known to be essential for the high rates of CYC1 transcription increased transcription of the CYC7 gene to levels characteristic of CYC1 transcription. On the other hand, the insertion of random DNA fragments at the same position gave mostly decreased CYC7 transcription. In addition to these in vitro constructions, a mutant plasmid was selected which had increased CYC7 transcription. This mutation was caused by the insertion of the bacterial IS1 element 313 by 5' to the CYC7 coding sequence. The significance of these results is discussed in terms of two alternative models for CYC7 gene expression.

Global DNA methylation remodeling accompanies CD8 T cell effector function

The differentiation of CD8 T cells in response to acute infection results in the acquisition of hallmark phenotypic effector functions; however, the epigenetic mechanisms that program this differentiation process on a genome-wide scale are largely unknown. In this article, we report the DNA methylomes of Ag-specific naive and day-8 effector CD8 T cells following acute lymphocytic choriomeningitis virus infection. During effector CD8 T cell differentiation, DNA methylation was remodeled such that changes in DNA methylation at gene promoter regions correlated negatively with gene expression. Importantly, differentially methylated regions were enriched at cis-elements, including enhancers active in naive T cells. Differentially methylated regions were associated with cell type-specific transcription factor binding sites, and these transcription factors clustered into modules that define networks targeted by epigenetic regulation and control of effector CD8 T cell function. Changes in the DNA methylation profile following CD8 T cell activation revealed numerous cellular processes, cis-elements, and transcription factor networks targeted by DNA methylation. Together, the results demonstrated that DNA methylation remodeling accompanies the acquisition of the CD8 T cell effector phenotype and repression of the naive cell state. Therefore, these data provide the framework for an epigenetic mechanism that is required for effector CD8 T cell differentiation and adaptive immune responses.

Cutting edge: Prolonged exposure to HIV reinforces a poised epigenetic program for PD-1 expression in virus-specific CD8 T cells

Ag-specific CD8 T cells play a critical role in controlling HIV infection but eventually lose antiviral functions in part because of expression and signaling through the inhibitory programmed death-1 (PD-1) receptor. To better understand the impact of prolonged TCR ligation on regulation of PD-1 expression in HIV-specific CD8 T cells, we investigated the capacity of virus-specific CD8 T cells to modify the PD-1 epigenetic program after reduction in viral load. We observed that the transcriptional regulatory region was unmethylated in the PD-1(hi) HIV-specific CD8 T cells, whereas it remained methylated in donor-matched naive cells at acute and chronic stages of infection. Surprisingly, the PD-1 promoter remained unmethylated in HIV-specific CD8 T cells from subjects with a viral load controlled by antiviral therapy for >2 y or from elite controllers. Together, these data demonstrate that the epigenetic program at the PD-1 locus becomes fixed after prolonged exposure to HIV virus.

Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence

Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10⁻¹⁵). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant F_ST (p = 0.00003) and positive Tajima's D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human–Neandertal divergence and is evolving under balancing selection, especially among European populations.

Natural selection shapes the genome in a non-random way, as an allele that contributes more to the reproductive fitness of a species increases in frequency within the population. Under balancing selection, a particular kind of natural selection, more than one allele increases in frequency in the population, likely due to a reproductive advantage of individuals carrying both alleles. Only a handful of loci have been well documented to evolve under balancing selection, with the HBB gene (sickle cell locus) being the best studied. Here, we report a non-coding (but putatively functional) locus that has maintained two divergent alleles in the human population since before the Human–Neandertal divergence and is therefore likely to be under balancing selection. These findings also provide a clear example for ancient African substructure.

The role of innate and adaptive immunity in Parkinson's disease

In recent years, inflammation has become implicated as a major pathogenic factor in the onset and progression of Parkinson's disease. Understanding the precise role for inflammation in PD will likely lead to understanding of how sporadic disease arises. In vivo evidence for inflammation in PD includes microglial activation, increased expression of inflammatory genes in the periphery and in the central nervous system (CNS), infiltration of peripheral immune cells into the CNS, and altered composition and phenotype of peripheral immune cells. These findings are recapitulated in various animal models of PD and are reviewed herein. Furthermore, we examine the potential relevance of PD-linked genetic mutations to altered immune function and the extent to which environmental exposures that recapitulate these phenotypes, which may lead to sporadic PD through similar mechanisms. Given the implications of immune system involvement on disease progression, we conclude by reviewing the evidence supporting the potential efficacy of immunomodulatory therapies in PD prevention or treatment. There is a clear need for additional research to clarify the role of immunity and inflammation in this chronic, neurodegenerative disease.

ZBTB32 is an early repressor of the CIITA and MHC class II gene expression during B cell differentiation to plasma cells

CIITA and MHC class II expression is silenced during the differentiation of B cells to plasma cells. When B cell differentiation is carried out ex vivo, CIITA silencing occurs rapidly, but the factors contributing to this event are not known. ZBTB32, also known as repressor of GATA3, was identified as an early repressor of CIITA in an ex vivo plasma cell differentiation model. ZBTB32 activity occurred at a time when B lymphocyte-induced maturation protein-1 (Blimp-1), the regulator of plasma cell fate and suppressor of CIITA, was minimally induced. Ectopic expression of ZBTB32 suppressed CIITA and I-A gene expression in B cells. Short hairpin RNA depletion of ZBTB32 in a plasma cell line resulted in re-expression of CIITA and I-A. Compared with conditional Blimp-1 knockout and wild-type B cells, B cells from ZBTB32/ROG-knockout mice displayed delayed kinetics in silencing CIITA during ex vivo plasma cell differentiation. ZBTB32 was found to bind to the CIITA gene, suggesting that ZBTB32 directly regulates CIITA. Lastly, ZBTB32 and Blimp-1 coimmunoprecipitated, suggesting that the two repressors may ultimately function together to silence CIITA expression. These results introduce ZBTB32 as a novel regulator of MHC-II gene expression and a potential regulatory partner of Blimp-1 in repressing gene expression.